Diagnostic work in SSMSE

This is all of the code that uses r4ss to pull individual runs from an SSMSE folder and looks closer at data that is not extracted in the summary function. It was starting to slow down my quarto document so I have moved it to this quarto document.

Pull data from SS runs

This chunk takes a while to run and pulls the ss_output data from all iterations and all scenarios, it only saves the data that is listed, so selectivity, catage, batage, natage, and new CPUE indexes.

Selectivity Exploration

Selectivity at length (points) with OM line

Selectivity at length (lines) with OM

Zoomed in Selectivity at length

Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Zoomed in Selectivity at length with highlighted line

Selectivity at age (points)

Selectivity at age (lines)

Zoomed in Selectivity at age

Zoomed in Selectivity at age with highlighted line

natage

N at age with OM (dashed)

N at age (lines) in 2017

N at age (points) in 2017

batage

Biomass at age (lines) with OM in 2017

Biomass at age (lines) in 2017

Biomass at age (points) in 2017

catage

Catch at age (lines) in 2017

Catch at age (points) in 2017

CPUE

commHL

commLL

Rec

SEAMAP_vid

SEAMAP_GF

NMFS_BLL

CBT_PRSurv

FWRI_RTD

Selectivity Exploration Disc

Selectivity at length (points)

Selectivity at length (lines)

Zoomed in Selectivity at length

Zoomed in Selectivity at length with highlighted line

Retention Exploration

Retention one iteration

Retention median

Ro Exploration

Extracted the R0 from SR_LN_R0 from the summary$scalar.